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.\" ========================================================================
.\"
.IX Title "SWISS::CCalt_prod 3pm"
.TH SWISS::CCalt_prod 3pm "2008-02-04" "perl v5.10.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "Name"
.IX Header "Name"
SWISS::CCalt_prod.pm
.SH "Description"
.IX Header "Description"
\&\fBSWISS::CCalt_prod\fR represents a comment on the topic '\s-1ALTERNATIVE\s0 \s-1PRODUCTS\s0'
within a Swiss-Prot or TrEMBL entry as specified in the user manual
http://www.expasy.org/sprot/userman.html .  Comments on other topics are stored
in other types of objects, such as \s-1SWISS::CC\s0 (see SWISS::CCs for more 
information).
.PP
Collectively, comments of all types are stored within a SWISS::CCs container
object.
.PP
\&\fBCode example\fR:
.PP
This example is given to illustrate the internal construction of an CCalt_prod
object.  However, for most purposes it should be possible to use the convenience
methods provided (e.g. the add, delete, get and set methods doocumented below)
instead of constructing the section manually.  The use of the convenience
methods is also recommended to ensure the structual integrity of the CCalt_prod
object.
.PP
.Vb 1
\& ## Create a new named isoform
\& 
\& my %thisFormHash;
\& 
\& ## give this some properties
\& 
\& # some properties are single data values
\& 
\& $thisFormHash{"Name"} = "This";
\& 
\& # some properties are lists of values
\&  
\& push @{$thisFormHash{"Synonyms"}}, "That";
\& push @{$thisFormHash{"Synonyms"}}, "The Other";
\& push @{$thisFormHash{"IsoId"}}, "P00000\-01";
\& push @{$thisFormHash{"IsoId"}}, "P00000\-02";
\& push @{$thisFormHash{"Sequence"}}, "VSP_000001";
\& push @{$thisFormHash{"Sequence"}}, "VSP_000002";
\& $thisFormHash{"Notes"} = "This local note";
\&  
\& ## put this form onto a list of all forms created by one type of event
\& 
\& my @newFormsList;
\& 
\& push @newFormsList, \e%thisFormHash;
\& 
\& ## put this list into a hash describing all characteristics of this event
\& 
\& my %eventHash;
\& $eventHash{"FormsList"} = \e@newFormsList;
\& 
\& ## set other values of this event
\& 
\& $eventHash{"Comment"} = "This Comment";
\& 
\& ## put the description of this event into a hash descrinbing all events
\& 
\& my %eventsHash;
\& $eventsHash{"Alternative splicing"} = \e%eventHash;
\& 
\& ## put a reference to this hash into the CCalt_products object
\& 
\& my $hashRef;
\& $hashRef = \e%eventsHash;
\& my $newCC = SWISS::CCalt_prod;
\& $newCC\->setEvents($hashRef);
\& $newCC\->toString();
.Ve
.PP
\&\fBMore simply, using the convenience methods addComment and addForm\fR:
.PP
.Vb 12
\& @synonyms = ("That", "The other");
\& @isoIds = ("P00000\-1", "P00000\-2");
\& @featIds = ("VSP_00001", "VSP_00002");
\& my $newCC = SWISS::CCalt_prod;
\& $newCC \-> addComment("Alternative splicing", "This comment");
\& $newCC \-> addForm("Alternative splicing", 
\&                   "This", 
\&                   \e@synonyms, 
\&                   \e@isoIds, 
\&                   \e@featIds,
\&                   "This local note");
\& print $newCC \-> toString();
.Ve
.PP
\&\fBOutput from both approaches:\fR
.PP
.Vb 6
\& CC   \-!\- ALTERNATIVE PRODUCTS:
\& CC        Event=Alternative splicing; Named isoforms=1;
\& CC          Comment=This comment.
\& CC        Name=This; Synonyms=That, The other;
\& CC          IsoId=P00000\-1, P00000\-2; Sequence=VSP_00001, VSP_00002;
\& CC          Note=This local note.
.Ve
.PP
\&\fBExample of adding evidence tags to a synonym\fR:
.PP
\&\f(CW$CC\fR \-> addEvidenceTag('\s-1EP8\s0', \*(L"Alternative splicing\*(R", \*(L"Synonyms\*(R", \*(L"\s-1VI\s0\*(R", \*(L"B\*(R");
.PP
to add the tag '\s-1EP8\s0' to synonym B of isoform \s-1VI\s0, produced by alternative
splicing
.PP
\&\fBHandling mutliple events\fR:
.PP
With the release of UniProt 8.0, the format of the \s-1CC\s0 \s-1ALTERNATIVE\s0 \s-1PRODUCTS\s0
blocks has changed slightly.  In particular, isoforms are no longer stored
according to the events that have generated them, so this:
.PP
.Vb 8
\& CC   \-!\- ALTERNATIVE PRODUCTS:
\& CC        Event=Alternative splicing; Named isoforms=1;
\& CC          Comment=This comment.
\& CC        Name=This; Synonyms=That, The other;
\& CC          IsoId=P00000\-1, P00000\-2; Sequence=VSP_00001, VSP_00002;
\& CC          Note=This local note.
\& CC        Event=Alternative initiation;
\& CC          Comment=Another comment.
.Ve
.PP
has become this:
.PP
.Vb 6
\& CC   \-!\- ALTERNATIVE PRODUCTS:
\& CC        Event=Alternative splicing, Alternative initation; Named isoforms=1;
\& CC          Comment=This comment. Another comment;
\& CC        Name=This; Synonyms=That, The other;
\& CC          IsoId=P00000\-1, P00000\-2; Sequence=VSP_00001, VSP_00002;
\& CC          Note=Produced by alternative splicing. This local note;
.Ve
.PP
The \s-1API\s0 is quite event-centric, reflecting the previous file format (where
different content was available according to the event type).  To get all
isoforms (for whatever events are annotated) under the new format, do:
.PP
.Vb 1
\& $CC\->keyEvent;
.Ve
.PP
which will return an arbitrary event that can be used a parameter in other
methods.  Any of the events annotated will function as parameters to retrieve
information about assocaticated isoforms: it is not necessary to supply the
complete list.
.SH "Inherits from"
.IX Header "Inherits from"
SWISS::BaseClass.pm
.SH "Attributes"
.IX Header "Attributes"
.IP "topic" 4
.IX Item "topic"
The topic of this comment ('\s-1ALTERNATIVE\s0 \s-1PRODUCTS\s0').
.SS "Standard methods"
.IX Subsection "Standard methods"
.IP "new" 4
.IX Item "new"
.PD 0
.IP "fromText" 4
.IX Item "fromText"
.PD
.SS "Reading/Writing methods"
.IX Subsection "Reading/Writing methods"
.IP "addEvent ($eventName)" 4
.IX Item "addEvent ($eventName)"
Allows the user to insert \*(L"events blocks\*(R" into the CCalt_prod object.
.ie n .IP "addEvidenceTag($tag, $event, $type, $name, $synonym)" 4
.el .IP "addEvidenceTag($tag, \f(CW$event\fR, \f(CW$type\fR, \f(CW$name\fR, \f(CW$synonym\fR)" 4
.IX Item "addEvidenceTag($tag, $event, $type, $name, $synonym)"
Add \f(CW$tag\fR to the tag list associated with the specified component of a CCalt_prod
object.  The event and type (of the item to which the tag is to be added, i.e.
\&\*(L"Comment\*(R", \*(L"Name\*(R", \*(L"Note\*(R", or \*(L"Synonyms\*(R") must always be specified: unless the
type is \*(L"Comment\*(R", the name must also be specifed (i.e. the contents of the Name
field for the isoform to which the tag is being attached); the name of the
synonym to which the tag are being attached must also be given if the type is
\&\*(L"Synonyms\*(R".
.ie n .IP "addForm ($eventName, $formName, \e@synonyms, \e@isoIds, \e@featIds, $note)" 4
.el .IP "addForm ($eventName, \f(CW$formName\fR, \e@synonyms, \e@isoIds, \e@featIds, \f(CW$note\fR)" 4
.IX Item "addForm ($eventName, $formName, @synonyms, @isoIds, @featIds, $note)"
Allows the user to add a form into a given event block.  See code example
(above) for more details.
.IP "deleteComment ($eventName)" 4
.IX Item "deleteComment ($eventName)"
Deletes the comment associated with this event.
.IP "deleteEvent ($eventName)" 4
.IX Item "deleteEvent ($eventName)"
Deletes an event from this CCalt_prod objects.
.ie n .IP "deleteEvidenceTag($tag, $event, $type, $name, $synonym)" 4
.el .IP "deleteEvidenceTag($tag, \f(CW$event\fR, \f(CW$type\fR, \f(CW$name\fR, \f(CW$synonym\fR)" 4
.IX Item "deleteEvidenceTag($tag, $event, $type, $name, $synonym)"
Deletes \f(CW$tag\fR from the tag list associated with the specified component of a
CCalt_prod object.  The event and type (of the item from which the tag is to be
deleted, i.e. \*(L"Comment\*(R", \*(L"Name\*(R", \*(L"Note\*(R", or \*(L"Synonyms\*(R") must always be
specified: unless the type is \*(L"Comment\*(R", the name must also be specifed (i.e.
the contents of the Name field for the isoform from which the tag is being
deleted); the name of the synonym from which the tag is being deleted must also
be given if the type is \*(L"Synonyms\*(R".
.ie n .IP "deleteForm ($eventName, $formName)" 4
.el .IP "deleteForm ($eventName, \f(CW$formName\fR)" 4
.IX Item "deleteForm ($eventName, $formName)"
Deletes a form associated with a given event.
.IP "keyEvent ()" 4
.IX Item "keyEvent ()"
Extracts one of the events annotated in this entry, which can then be used to
retrieve data associated with this event
.IP "getComment($eventName)" 4
.IX Item "getComment($eventName)"
Returns the comment for this event.
.IP "getEventNames" 4
.IX Item "getEventNames"
Returns a list of all event names for this CCalt_prod object.
.ie n .IP "getEvidenceTags($event, $type, $name, $synonym)" 4
.el .IP "getEvidenceTags($event, \f(CW$type\fR, \f(CW$name\fR, \f(CW$synonym\fR)" 4
.IX Item "getEvidenceTags($event, $type, $name, $synonym)"
Returns a list of the tags attached to the specified component of a  CCalt_prod
object. The event and type (of the item to which the tag is attached, i.e.
\&\*(L"Comment\*(R", \*(L"Name\*(R", \*(L"Note\*(R", or \*(L"Synonyms\*(R") must always be specified: unless the
type is \*(L"Comment\*(R", the name must also be specifed (i.e. the contents of the Name
field for the isoform whose tags are being fetched); the name of the synonym
whose tags are being fetched must also be given if the type is \*(L"Synonyms\*(R".
.ie n .IP "getEvidenceTagsString($event, $type, $name, $synonym)" 4
.el .IP "getEvidenceTagsString($event, \f(CW$type\fR, \f(CW$name\fR, \f(CW$synonym\fR)" 4
.IX Item "getEvidenceTagsString($event, $type, $name, $synonym)"
Returns the tags attached to the specified component of a CCalt_prod object as a
string literal. The event and type (of the item to which the tag is attached,
i.e. \*(L"Comment\*(R", \*(L"Name\*(R", \*(L"Note\*(R", or \*(L"Synonyms\*(R") must always be specified: unless
the type is \*(L"Comment\*(R", the name must also be specifed (i.e. the contents of the
Name field for the isoform whose tags are being fetched); the name of the
synonym whose tags are being fetched must also be given if the type is
\&\*(L"Synonyms\*(R".
.ie n .IP "getFeatIds ($eventName, $formName)" 4
.el .IP "getFeatIds ($eventName, \f(CW$formName\fR)" 4
.IX Item "getFeatIds ($eventName, $formName)"
Returns a list of all feature IDs associated with this form produced by this
event.
.IP "getFormNames ($eventName)" 4
.IX Item "getFormNames ($eventName)"
Returns a list of all form names for this form produced by this event.
.ie n .IP "getIsoIds ($eventName, $formName)" 4
.el .IP "getIsoIds ($eventName, \f(CW$formName\fR)" 4
.IX Item "getIsoIds ($eventName, $formName)"
Returns a list of all IsoIds for this form produced by this event.
.IP "getNamedFormCount($eventName)" 4
.IX Item "getNamedFormCount($eventName)"
Returns the number of named and identified forms for this event.
.ie n .IP "getNote ($eventName, $formName)" 4
.el .IP "getNote ($eventName, \f(CW$formName\fR)" 4
.IX Item "getNote ($eventName, $formName)"
Returns the local note of this form produced by this event.
.ie n .IP "getSynonyms ($eventName, $formName)" 4
.el .IP "getSynonyms ($eventName, \f(CW$formName\fR)" 4
.IX Item "getSynonyms ($eventName, $formName)"
Returns a list of all synonyms of this form produced by this event.
.ie n .IP "hasEvidenceTag ($tag, $event, $type, $name, $synonym)" 4
.el .IP "hasEvidenceTag ($tag, \f(CW$event\fR, \f(CW$type\fR, \f(CW$name\fR, \f(CW$synonym\fR)" 4
.IX Item "hasEvidenceTag ($tag, $event, $type, $name, $synonym)"
Returns 1 if the specified component of a CCalt_prod object has the specified
tag.  The event and type (of the item to which the tag is attached, i.e.
\&\*(L"Comment\*(R", \*(L"Name\*(R", \*(L"Note\*(R", or \*(L"Synonyms\*(R") must always be specified: unless the
type is \*(L"Comment\*(R", the name must also be specifed (i.e. the contents of the Name
field for the isoform whose tags are being fetched); the name of the synonym
whose tags are being fetched must also be given if the type is \*(L"Synonyms\*(R".
.ie n .IP "setComment ($eventName, $comment)" 4
.el .IP "setComment ($eventName, \f(CW$comment\fR)" 4
.IX Item "setComment ($eventName, $comment)"
.Vb 1
\&  Allows the user to add a global comment for a particular event.
.Ve
.ie n .IP "setEvidenceTags(\e@tags, $event, $type, $name, $synonym)" 4
.el .IP "setEvidenceTags(\e@tags, \f(CW$event\fR, \f(CW$type\fR, \f(CW$name\fR, \f(CW$synonym\fR)" 4
.IX Item "setEvidenceTags(@tags, $event, $type, $name, $synonym)"
Sets the evidence tags of the specified component of a CCalt_prod object to the
array pointed to by \e@tags.  The event and type (of the item to which the tag
are to be added, i.e. \*(L"Comment\*(R", \*(L"Name\*(R", \*(L"Note\*(R", or \*(L"Synonyms\*(R") must always be
specified: unless the type is \*(L"Comment\*(R", the name must also be specifed (i.e.
the contents of the Name field for the isoform to which tags are being
attached); the name of the synonym to which tags are being attached must also be
given if the type is \*(L"Synonyms\*(R".
.IP "setEvent (%eventHash)" 4
.IX Item "setEvent (%eventHash)"
Can be used to manually insert a hash representing one event.  Use of this
method is not recommeded, see code examples for how to use the convenience
methods to create a CCalt_prod object.
.ie n .IP "setFeatIds($eventName, $oldName, \e@featIds)" 4
.el .IP "setFeatIds($eventName, \f(CW$oldName\fR, \e@featIds)" 4
.IX Item "setFeatIds($eventName, $oldName, @featIds)"
Sets the feature Ids for the named form (associated with the specified event) to
the supplied list.
.ie n .IP "setFormName($eventName, $oldName, $newName)" 4
.el .IP "setFormName($eventName, \f(CW$oldName\fR, \f(CW$newName\fR)" 4
.IX Item "setFormName($eventName, $oldName, $newName)"
Changes the name of the formed named \f(CW$OldName\fR, associated with this event, to
the \f(CW$newName\fR.
.ie n .IP "setIsoIds($eventName, $oldName, \e@isoIds)" 4
.el .IP "setIsoIds($eventName, \f(CW$oldName\fR, \e@isoIds)" 4
.IX Item "setIsoIds($eventName, $oldName, @isoIds)"
Sets the Isoform Ids for the named form (associated with the specified event) to
the supplied list.
.ie n .IP "setNote($eventName, $name, $note)" 4
.el .IP "setNote($eventName, \f(CW$name\fR, \f(CW$note\fR)" 4
.IX Item "setNote($eventName, $name, $note)"
Sets the local note for the named form (associated with the specified event).
.ie n .IP "setSynonyms($eventName, $name, \e@synonyms)" 4
.el .IP "setSynonyms($eventName, \f(CW$name\fR, \e@synonyms)" 4
.IX Item "setSynonyms($eventName, $name, @synonyms)"
Sets the synonyms for the named form (associated with the specified event) to
the supplied list.
.IP "toString" 4
.IX Item "toString"
Returns a string representation of this comment.
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 1540:" 4
.IX Item "Around line 1540:"
=back doesn't take any parameters, but you said =back  =head1 Methods